I'm afraid that the methodology has been shown to be inadequate in the case of a number of projects, including the Borders railway, and as such, I believe it is holding back the development of the network. It wasn't even seen as adequate for HS2 as I recall, therefore why is it adequate for local routes ?You can argue about the methodology all you like, but it is...
a) what it is
b) consistent between all modes
c) by a long way better for rail than the methodology used pre-1997
d) a well developed, researched and econometric method of assessment
To say outputs of a business case using this assessment method are 'meaningless' and 'aren't worth the paper they're written on' is, frankly, an insult to the dozens of transport professionals and politicians (of all the main parties) who developed and improved the assessment methodology over the past two decades. Let alone the hundreds of people who spend their working lives using the assessment methodology to justify projects and secure funding for thousands of transport projects every year that benefit society.
I would hope that those with power within the railway industry are strongly advocating a review to central Government at every opportunity, in the light of experience with the Borders line and South Wales etc.